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Oceanographic Data Sources, Data Management, And Software Tools
For Marine Mammal Modeling
Mark Baumgartner Woods Hole Oceanographic Institution
1) Oceanographic Data Sources • In-situ • Remotely-sensed • Climatologies • Ocean Models • Static
2) Data Management • Metadata • Data Formats
3) Software • Processing • Plotting/Visualization • Analysis/Statistics
1) Oceanographic Data Sources • In-situ • Remotely-sensed • Climatologies • Ocean Models • Static
2) Data Management • Metadata • Data Formats
3) Software • Processing • Plotting/Visualization • Analysis/Statistics
• Along-track • Profiled • Tow-yo’ed • Moored
• Along-track • Profiled • Tow-yo’ed • Moored
Primary Measurements Water Depth Temperature
Salinity Currents
Fluorescence Zooplankton
Acoustic Backscatter
• Along-track • Profiled • Tow-yo’ed • Moored
Scientific Echosounder
Acoustic Doppler Current Profiler
Thermosalinograph
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• Along-track • Profiled • Tow-yo’ed • Moored
CTD
Optical Plankton Counter
Video Plankton Recorder Acoustic
Doppler Current Profiler
Conductivity Temperature
Depth Instrument (CTD)
Fluorometer
• Along-track • Profiled • Tow-yo’ed • Moored
Seasoar
Acrobat
Scanfish
BIOMAPER
• Along-track • Profiled • Tow-yo’ed • Moored
You are here (San Diego)
3 m NDBC discus buoy Resources
• Instrumentation → Oceanographers → Instrument Manufacturers
• Data Archives → National Oceanographic Data Center
(www.nodc.noaa.gov) → National Data Buoy Center (www.ndbc.noaa.gov)
1) Oceanographic Data Sources • In-situ • Remotely-sensed • Climatologies • Ocean Models • Static
2) Data Management • Metadata • Data Formats
3) Software • Processing • Plotting/Visualization • Analysis/Statistics
• Passive → Sea surface
temperature (AVHRR)
→ Ocean color (SeaWiFS)
• Active → Sea surface height
(TOPEX/Poseidon) → Winds (QuikSCAT)
TOPEX/Poseidon
AVHRR
SeaWiFS QuikSCAT
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Coverage: Global Resolution: 18 km
Available: Weekly
Coverage: Local Resolution: 1 km
Available: ~twice daily
Resources
• Sea surface temperature → JPL Data Archive (poet.jpl.nasa.gov; podaac-
www.jpl.nasa.gov/sst) → NOAA Coastwatch (coastwatch.noaa.gov)
• Ocean Color → NASA SeaWiFS (reason.gsfc.nasa.gov/OPS/Giovanni/
ocean.seawifs.shtml)
• Sea Surface Height → JPL Data Archive (poet.jpl.nasa.gov) → Aviso (www.aviso.oceanobs.com)
1) Oceanographic Data Sources • In-situ • Remotely-sensed • Climatologies • Ocean Models • Static
2) Data Management • Metadata • Data Formats
3) Software • Processing • Plotting/Visualization • Analysis/Statistics
Climatology: Long-term average conditions
Anomaly: Deviation from the long-term average conditions
Surface Salinity Climatology from World Ocean Atlas
Salinity at 1000 m Climatology from World Ocean Atlas
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Ullman, D.S. and P.C. Cornillon. 1999. Satellite derived sea surface temperature fronts on the continental shelf off the northeast U.S.
coast. Journal of Geophysical Research 104:23459-23478.
Surface Temperature Front Climatology Resources
• Global Climatology → World Ocean Database and World Ocean Atlas
(www.nodc.noaa.gov/OC5/indprod.html)
• Regional or Local Climatology → Find in the literature and request data from authors
1) Oceanographic Data Sources • In-situ • Remotely-sensed • Climatologies • Ocean Models • Static
2) Data Management • Metadata • Data Formats
3) Software • Processing • Plotting/Visualization • Analysis/Statistics
?
Back in the day…
Today…
Model Surface Currents in the Northwest Atlantic from the NOAA Regional
Ocean Forecast System
Resources
• Global Models → U.S. Navy Models (www7320.nrlssc.navy.mil/
global_nlom)
• Regional Models → U.S. East Coast Regional Ocean Forecast Model
(polar.ncep.noaa.gov/cofs)
• Local Models → Find local modelers and build collaborations
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1) Oceanographic Data Sources • In-situ • Remotely-sensed • Climatologies • Ocean Models • Static
2) Data Management • Metadata • Data Formats
3) Software • Processing • Plotting/Visualization • Analysis/Statistics
• Bathymetry • Coastlines
Resources
• High-resolution bathymetry (ETOPO5, ETOPO2, SRTM30_PLUS) → Scripps Institution of Oceanography (topex.ucsd.edu/
WWW_html/mar_topo.html) → U.S. National Geophysical Data Center
(www.ngdc.noaa.gov/mgg/global/global.html)
• Coastlines → U.S. National Geophysical Data Center
(www.ngdc.noaa.gov/mgg/shorelines/shorelines.html)
1) Oceanographic Data Sources • In-situ • Remotely-sensed • Climatologies • Ocean Models • Static
2) Data Management • Metadata • Data Formats
3) Software • Processing • Plotting/Visualization • Analysis/Statistics
Metadata: “Data about data” Metadata: “Data about data”
Why collect data about your data?
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Metadata: “Data about data”
Why collect data about your data? • Because you’ll forget!!! • Facilitates data sharing – your collaborators will
thank you
Kinds of things to include in your metadata… • Project name • Geographic area • Species of interest • Platform • Who collected the data (e.g., name, organization) • Kind of data (e.g., salinity) • Type of instrument (what it is, model, serial
number) • What kind of processing has been done to the raw
data
Resources
• Metadata standards → Federal Geographic Data Committee Metadata Standard
(www.fgdc.gov/index.html)
1) Oceanographic Data Sources • In-situ • Remotely-sensed • Climatologies • Ocean Models • Static
2) Data Management • Metadata • Data Formats
3) Software • Processing • Plotting/Visualization • Analysis/Statistics
Which data format? • Appropriateness for your data • Ease of use • Flexibility • Portability • Ability to accommodate metadata • Data easily transferred to collaborators
Which data format? • ASCII (text) files • Proprietary formats (Arc) • Relational databases • Scientific formats
→ HDF → NetCDF
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Which data format? • ASCII (text) files • Proprietary formats (Arc) • Relational databases • Scientific formats
→ HDF → NetCDF
NetCDF • Stores multidimensional
array data • Excellent capacity for
metadata • Platform-independent
(can share between any machine)
• No compression (may not be the format of choice for archiving)
Resources
• Scientific data formats → HDF (hdf.ncsa.uiuc.edu) → NetCDF (www.unidata.ucar.edu/software/netcdf)
1) Oceanographic Data Sources • In-situ • Remotely-sensed • Climatologies • Ocean Models • Static
2) Data Management • Metadata • Data Formats
3) Software • Processing • Plotting/Visualization • Analysis/Statistics
Processing Software that will allow you to prepare your data for visualization and analysis
Ideally, should be flexible to deal with any and all features and idiosyncrasies in your data
→ Extract regions of interest in satellite data → Extract features in in-situ data → Editing/quality controlling sighting data
Resources
• Processing → Matlab (www.mathworks.com) → IDL (www.rsinc.com/idl) → Perl (www.perl.org) → ArcView/ArcGIS (www.esri.com) → IDRISI (www.clarklabs.org)
1) Oceanographic Data Sources • In-situ • Remotely-sensed • Climatologies • Ocean Models • Static
2) Data Management • Metadata • Data Formats
3) Software • Processing • Plotting/Visualization • Analysis/Statistics
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Plotting/Visualization Software that will allow you to qualitatively examine your data AND convey your results in public communications (presentations and papers)
Ideally, should be flexible to deal with any and all features and idiosyncrasies in your data
→ Plot maps of distributions → Plot environmental data in whatever form
it comes in (e.g., temperature profiles) → Plot relationships between variables
Resources • GIS
→ ArcView/ArcGIS (www.esri.com) → GRASS (grass.itc.it) → MapInfo (www.mapinfo.com) → Others (see software.geocomm.com)
• Mapping → Generic Mapping Tools (GMT) (gmt.soest.hawaii.edu) → Online Map Creation (www.aquarius.geomar.de/omc) → Planiglobe (www.planiglobe.com/omc_set.html)
• Analytical software with plotting/visualization capabilities → Matlab (www.mathoworks.com) → IDL (www.rsinc.com/idl)
1) Oceanographic Data Sources • In-situ • Remotely-sensed • Climatologies • Ocean Models • Static
2) Data Management • Metadata • Data Formats
3) Software • Processing • Plotting/Visualization • Analysis/Statistics
Analysis/Statistics Software that will allow you to quantitatively examine your data
Must have the tools you need → Basic statistics (t-test, ANOVA) → Advanced regression models (GLM, GAM) → Community analyses
Resources
• Analysis/Statistics → R (www.r-project.org) → Splus (www.insightful.com/products/splus) → SAS (www.sas.com) → Matlab (www.mathoworks.com) → IDL (www.rsinc.com/idl) → ArcView/ArcGIS (www.esri.com)
Final thoughts on software…
• Beware of “push-button” processing and analysis – make sure you know what’s going on behind the scenes
• Learn to program a computer → C, FORTRAN, BASIC → Matlab, IDL → Arc → Perl
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Thanks to my fellow Workshop Organizing Committee members… • Ed Gregr • Toshihide Hamzaki • Ellen Hines • Kristin Laidre • Daniel Palacios • Jessica Redfern • Kathleen Vigness Raposa
This presentation available at ftp://ftp.whoi.edu/pub/users/mbaumgartner/baumgartner_modeling.ppt
dimensions: n = 179 ; variables: float depth(n) ; depth:long_name = "depth" ; depth:units = "meters" ; float temp(n) ; temp:long_name = "temperature" ; temp:units = "degC" ; float sal(n) ; sal:long_name = "salinity" ; sal:units = "PSU" ;
// global attributes: :experiment = "North Atlantic Right Whale Ecology" ; :platform = "NOAA Ship Albatross IV" ; :cruise = "AL0504" ; :instrument_type = "SBE 19plus CTD" ; :serial_number = 4501 ; :comments = "CTD data for cast 186" ; :cast = 186 ; :date = "05/19/05 18:00:00" ; :lon = -69.2037 ; :lat = 41.2932 ; :water_depth = 98.0 ; :designation = "DV40" ; :set_ctd_flag_min_speed = 0.3 ;
NetCDF header
Loder, J.W., G. Han, C.G. Hannah, D.A. Greenberg and P.C. Smith. 1997. Hydrography and baroclinic circulation in the Scotian Shelf region: winter
versus summer. Canadian Journal of Fisheries and Aquatic Sciences 54:40-56.
Summer Climatology of Bottom Temperature and Salinity